Project abstract for group thomasdd

Structural Dynamics of Muscle Proteins

The goal of this research is to understand the structural dynamics associated with force-generating proteins during muscle contraction and to elucidate the molecular mechanisms and regulation of pumps and channels that controls the calcium uptake and release into the sarcoplasmic reticulum and thus control the contraction and relaxation of the muscle. Structural and functional models, derived from structural information from x-ray crystallography and electron microscopy, are tested experimentally by an approach based on site-directed labeling and EPR and fluorescence spectroscopy. Specifically, structural models of conformational transitions in muscle proteins are tested and refined by results from the spectroscopic techniques with the aim to detect biologically relevant protein motions. No single method can provide needed information about changes in structure and interactions that occur under functional conditions; a multidisciplinary approach is needed. This group's approach includes computational simulations that are necessary to connect atomistic models with experiment.

The computational methods used include ab initio quantum chemistry calculations of spectroscopic probes and molecular dynamics simulations of proteins labeled with these probes. From these simulations the researchers can determine parameters that can be used to interpret in a structural context experimental data from fluorescence and EPR spectroscopy. For example, Monte-Carlo type simulations are used to study the conformation of fluorescent fusions protein constructs. Predicted FRET data is calculated from multiple simulations starting from different structural states of SERCA. Long, µs, all-atom molecular dynamics simulations have been performed to study the effect of ligand binding on the domain dynamics of SERCA. The simulations and experimental data suggest that large-scale open-to-closed functional conformational transitions occur. These simulations helped the researchers determine thermodynamic properties important for the understanding of the protein function.